Docking heparan sulfate-based ligands as a promising inhibitor for SARS-CoV-2.

Publication date: Dec 12, 2024

Heparan sulfate (HS) linear polysaccharide glycosaminoglycan compound is linked to components from the cell surface and the extracellular matrix. HS mediates SARS-CoV-2 infection through spike protein binding to cell surface receptors and is required to bind ACE2, prompting the need for electronic structure and molecular docking evaluation of this core system to exploit this attachment in developing new derivatives. Therefore, we have studied five molecules based on HS using molecular docking and electronic structure analysis. Non-covalent interaction analysis shows hydrogen bonding and van der Waals interactions in the binding to RBD-ACE2 interface and 3CL. SDM3 and SDM1 molecules present the lowest gap, including solvent effect under 154. 6 kcal/mol, and exhibit the most reactivity behavior in this group, potentially leading to enhanced interaction in docking studies. Heparan sulfate and four derivatives were optimized using B3LYP functional with two basis sets 6-31 + G(d,p) and def2SVP. Electronic structure was used to explore the main interactions and the reactivity of these molecules, and these optimized structures were used in the molecular docking study against 3CL, RBD, and ACE2.

Concepts Keywords
Def2svp ACE2 protein, human
Docking Angiotensin-Converting Enzyme 2
Glycosaminoglycan Angiotensin-Converting Enzyme 2
Promising Antiviral Agents
Solvent Antiviral Agents
B3LYP
Binding Sites
Coronavirus 3C Proteases
Coronavirus 3C Proteases
COVID-19
COVID-19 Drug Treatment
Heparan sulfate
Heparitin Sulfate
Heparitin Sulfate
Humans
Hydrogen Bonding
Ligands
Ligands
Molecular docking
Molecular Docking Simulation
Protein Binding
SARS-CoV-2
SARS-CoV-2
Spike Glycoprotein, Coronavirus
Spike Glycoprotein, Coronavirus
spike protein, SARS-CoV-2

Semantics

Type Source Name
disease MESH SARS-CoV-2 infection
pathway REACTOME SARS-CoV-2 Infection

Original Article

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